How can I apply decimate modifier to multple files and save them as a different file automatically?
Ok, I wrote a script for my purpose. Maybe it will be helpful for somebody.

Here is the python script that decimates model and save as a new file.
You can change iteration and decimateRatio

import bpy
import os

##Cleans all decimate modifiers
def cleanAllDecimateModifiers(obj):
    for m in obj.modifiers:
        if(m.type=="DECIMATE"):
#           print("Removing modifier ")
            obj.modifiers.remove(modifier=m)


numberOfIteration=2
decimateRatio=0.3
modifierName='DecimateMod'

for i in range(0,numberOfIteration):
    objectList=bpy.data.objects
    for obj in objectList:
        if(obj.type=="MESH"):


            cleanAllDecimateModifiers(obj)

            modifier=obj.modifiers.new(modifierName,'DECIMATE')
            modifier.ratio=1-decimateRatio*(i+1)
            modifier.use_collapse_triangulate=True

    fileName=bpy.data.filepath
    fileName=os.path.splitext(fileName)[0]

    #Trim decimate version of file name
    indexOf_=fileName.rfind('_')
    if(indexOf_!=-1 and fileName[indexOf_]+fileName[indexOf_+1]=="_d"):
        fileName=fileName.split("_d")[0]


    fileName='{}{}{}{}'.format(fileName, "_d",str(i+2),".blend")

    bpy.ops.wm.save_as_mainfile(filepath=fileName)


Also you can run this script with a bash command for all child files having .blend extension.

find . -name '*.blend' -exec blender {} --background --python myScript.py \;


Thanks to Attie for bash command